[med-svn] r5178 - in trunk/packages/ensembl/ensembl/57/debian: . patches
Steffen Möller
moeller at alioth.debian.org
Fri Aug 20 23:12:29 UTC 2010
Author: moeller
Date: 2010-08-20 23:12:28 +0000 (Fri, 20 Aug 2010)
New Revision: 5178
Removed:
trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1
Modified:
trunk/packages/ensembl/ensembl/57/debian/
trunk/packages/ensembl/ensembl/57/debian/patches/series
Log:
Preparing for svn-buildpackage
Property changes on: trunk/packages/ensembl/ensembl/57/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Deleted: trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log 2010-08-20 22:57:12 UTC (rev 5177)
+++ trunk/packages/ensembl/ensembl/57/debian/ensembl.debhelper.log 2010-08-20 23:12:28 UTC (rev 5178)
@@ -1,43 +0,0 @@
-dh_prep
-dh_installchangelogs
-dh_installdocs
-dh_installexamples
-dh_install
-dh_installman
-dh_installinit
-dh_strip
-dh_compress
-dh_fixperms
-dh_perl
-dh_installdeb
-dh_gencontrol
-dh_md5sums
-dh_builddeb
-dh_installchangelogs
-dh_installdocs
-dh_installexamples
-dh_install
-dh_installman
-dh_installinit
-dh_strip
-dh_compress
-dh_fixperms
-dh_perl
-dh_installdeb
-dh_gencontrol
-dh_md5sums
-dh_builddeb
-dh_installchangelogs
-dh_installdocs
-dh_installexamples
-dh_install
-dh_installman
-dh_installinit
-dh_strip
-dh_compress
-dh_fixperms
-dh_perl
-dh_installdeb
-dh_gencontrol
-dh_md5sums
-dh_builddeb
Deleted: trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1 2010-08-20 22:57:12 UTC (rev 5177)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/debian-changes-57-1 2010-08-20 23:12:28 UTC (rev 5178)
@@ -1,2335 +0,0 @@
-Description: Upstream changes introduced in version 57-1
- This patch has been created by dpkg-source during the package build.
- Here's the last changelog entry, hopefully it gives details on why
- those changes were made:
- .
- ensembl (57-1) unstable; urgency=low
- .
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
- .
- The person named in the Author field signed this changelog entry.
-Author: Richard Holland <holland at eaglegenomics.com>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Origin: <vendor|upstream|other>, <url of original patch>
-Bug: <url in upstream bugtracker>
-Bug-Debian: http://bugs.debian.org/<bugnumber>
-Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
-Forwarded: <no|not-needed|url proving that it has been forwarded>
-Reviewed-By: <name and email of someone who approved the patch>
-Last-Update: <YYYY-MM-DD>
-
---- ensembl-57.orig/ensembl-compara/modules/t/CreateComparaTestDatabase.pl
-+++ ensembl-57/ensembl-compara/modules/t/CreateComparaTestDatabase.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # File name: CreateCoreTestDatabase.pl
- #
---- ensembl-57.orig/ensembl-compara/modules/t/CreateCoreTestDatabase.pl
-+++ ensembl-57/ensembl-compara/modules/t/CreateCoreTestDatabase.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # File name: CreateCoreTestDatabase.pl
- #
---- ensembl-57.orig/ensembl-compara/sql/UpdatePrefilledTable.pl
-+++ ensembl-57/ensembl-compara/sql/UpdatePrefilledTable.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #
- # updates the external db tables on all of the core databases on a given host
---- ensembl-57.orig/ensembl-compara/scripts/domain/ImportDomainFromCoreDB.pl
-+++ ensembl-57/ensembl-compara/scripts/domain/ImportDomainFromCoreDB.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::ExternalData::Family::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/tree/testTaxonTree.pl
-+++ ensembl-57/ensembl-compara/scripts/tree/testTaxonTree.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/tree/dumpTreeMSA.pl
-+++ ensembl-57/ensembl-compara/scripts/tree/dumpTreeMSA.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/tree/geneTreeTool.pl
-+++ ensembl-57/ensembl-compara/scripts/tree/geneTreeTool.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/misc/ConvertChimpCoordsScaffold2Chromosome.pl
-+++ ensembl-57/ensembl-compara/scripts/misc/ConvertChimpCoordsScaffold2Chromosome.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/misc/comparaUpdateStrand.pl
-+++ ensembl-57/ensembl-compara/scripts/misc/comparaUpdateStrand.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/taxonomy/mysqldumpGenomeDBNcbiTaxa.pl
-+++ ensembl-57/ensembl-compara/scripts/taxonomy/mysqldumpGenomeDBNcbiTaxa.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/taxonomy/taxonTreeTool.pl
-+++ ensembl-57/ensembl-compara/scripts/taxonomy/taxonTreeTool.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Switch;
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAxtAlignments.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpAxtAlignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/dumps/dumpTransAxt.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/dumpTransAxt.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpFakeMultiAlign.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpFakeMultiAlign.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- my $description = q{
- ###########################################################################
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpMultiAlign.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpMultiAlign.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- my $description = q{
- ###########################################################################
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAlignSlice.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpAlignSlice.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- my $description = q{
- ###########################################################################
---- ensembl-57.orig/ensembl-compara/scripts/dumps/LoadAxtAlignments.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/LoadAxtAlignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpChromosomeFragments.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpChromosomeFragments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
-
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpandLoadChromosomeFragments.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpandLoadChromosomeFragments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAlignments.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpAlignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Registry;
---- ensembl-57.orig/ensembl-compara/scripts/dumps/DumpAlignedGenes.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/DumpAlignedGenes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/dumps/fetch_alignblocks.pl
-+++ ensembl-57/ensembl-compara/scripts/dumps/fetch_alignblocks.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/synteny/DumpGFFAlignmentsForSynteny.pl
-+++ ensembl-57/ensembl-compara/scripts/synteny/DumpGFFAlignmentsForSynteny.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Registry;
---- ensembl-57.orig/ensembl-compara/scripts/synteny/getsynteny.pl
-+++ ensembl-57/ensembl-compara/scripts/synteny/getsynteny.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/synteny/LoadSyntenyData.pl
-+++ ensembl-57/ensembl-compara/scripts/synteny/LoadSyntenyData.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-compara/scripts/synteny/DumpGFFHomologuesForSynteny.pl
-+++ ensembl-57/ensembl-compara/scripts/synteny/DumpGFFHomologuesForSynteny.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Registry;
---- ensembl-57.orig/ensembl-compara/scripts/homology/InsertParaloguesPrediction.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/InsertParaloguesPrediction.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/getHomologyAlignment.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/getHomologyAlignment.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/generate_dN_dS.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/generate_dN_dS.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/detectSplitGenes.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/detectSplitGenes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/comparaDirectLoadHomology.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/comparaDirectLoadHomology.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/homology/transfer_homologies.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/transfer_homologies.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/DumpUpstreamGenes.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/DumpUpstreamGenes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/generate_dN_dS_stats.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/generate_dN_dS_stats.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/homology/LaunchPromoterwise.pl
-+++ ensembl-57/ensembl-compara/scripts/homology/LaunchPromoterwise.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- #use Bio::EnsEMBL::Pipeline::Tools::Promoterwise;
---- ensembl-57.orig/ensembl-compara/scripts/blastz/LaunchBlastz.pl
-+++ ensembl-57/ensembl-compara/scripts/blastz/LaunchBlastz.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Pipeline::Runnable::Blastz;
---- ensembl-57.orig/ensembl-compara/scripts/blastz/LoadUcscNetData.pl
-+++ ensembl-57/ensembl-compara/scripts/blastz/LoadUcscNetData.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- my $description = q{
- ###########################################################################
---- ensembl-57.orig/ensembl-compara/scripts/blastz/filter_blastz.pl
-+++ ensembl-57/ensembl-compara/scripts/blastz/filter_blastz.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
- $|=1;
---- ensembl-57.orig/ensembl-compara/scripts/compare/homology_diff3.pl
-+++ ensembl-57/ensembl-compara/scripts/compare/homology_diff3.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- =head1
- this script does homology dumps generated with this SQL statement from two different
- compara databases and compares them for differences.
---- ensembl-57.orig/ensembl-compara/scripts/compare/homology_diff.pl
-+++ ensembl-57/ensembl-compara/scripts/compare/homology_diff.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- =head1
- this script does homology dumps generated with this SQL statement from two different
- compara databases and compares them for differences.
---- ensembl-57.orig/ensembl-compara/scripts/family/InsertRedundantPeptidesAndGenesInFamilies.pl
-+++ ensembl-57/ensembl-compara/scripts/family/InsertRedundantPeptidesAndGenesInFamilies.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/family/parse_mcl.pl
-+++ ensembl-57/ensembl-compara/scripts/family/parse_mcl.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/family/consensifier.pl
-+++ ensembl-57/ensembl-compara/scripts/family/consensifier.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- # $Id: consensifier.pl,v 1.3 2005-01-14 15:57:25 abel Exp $
- #
- # Derives consensus annotations from descriptions in a database, using a
---- ensembl-57.orig/ensembl-compara/scripts/family/assemble-consensus.pl
-+++ ensembl-57/ensembl-compara/scripts/family/assemble-consensus.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- # Script to assemble the consensus annotations from different files into
- # final ones. It basically takes the SWISS-PROT description consensus if
---- ensembl-57.orig/ensembl-compara/scripts/family/LoadDescriptionInFamily.pl
-+++ ensembl-57/ensembl-compara/scripts/family/LoadDescriptionInFamily.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessMethodLinkSpeciesSet.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessMethodLinkSpeciesSet.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessMember.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessMember.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessMember2.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessMember2.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/getConservationScores.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getConservationScores.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Registry;
---- ensembl-57.orig/ensembl-compara/scripts/examples/getHomologyCluster2.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getHomologyCluster2.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/getHomology_GenomicAlignBlocks.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getHomology_GenomicAlignBlocks.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/getHomology_DnaAlignFeatures.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getHomology_DnaAlignFeatures.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessDnaFrag.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessDnaFrag.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology2.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology2.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology_distances.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology_distances.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
- use Bio::TreeIO;
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology12.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology12.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology14.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology14.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/getHomology.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getHomology.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology15.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology15.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology_exon_alignments.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology_exon_alignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/checkComparaRegistryConf.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/checkComparaRegistryConf.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessGenomeDB.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessGenomeDB.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/getHomologyCluster.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getHomologyCluster.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/api_speed_test.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/api_speed_test.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology13.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology13.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessGenomicAlignBlocks2.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessGenomicAlignBlocks2.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/homology8.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/homology8.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use Bio::EnsEMBL::Registry;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/accessGenomicAlignBlocks.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/accessGenomicAlignBlocks.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/getFamily.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getFamily.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/get_interpro_alignments.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/get_interpro_alignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use warnings;
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/examples/getHomologyAligns.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/getHomologyAligns.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test4.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test4.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test2.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test2.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test3.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test3.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/examples/exercise_answers/test1.pl
-+++ ensembl-57/ensembl-compara/scripts/examples/exercise_answers/test1.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/BLAT/parse_and_score.pl
-+++ ensembl-57/ensembl-compara/scripts/BLAT/parse_and_score.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
- use strict;
---- ensembl-57.orig/ensembl-compara/scripts/BLAT/run_BLAT_pipeline.pl
-+++ ensembl-57/ensembl-compara/scripts/BLAT/run_BLAT_pipeline.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/BLAT/LaunchBLAT.pl
-+++ ensembl-57/ensembl-compara/scripts/BLAT/LaunchBLAT.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
- =head1 NAME
---- ensembl-57.orig/ensembl-compara/scripts/BLAT/Exon_stats_parse_and_score.pl
-+++ ensembl-57/ensembl-compara/scripts/BLAT/Exon_stats_parse_and_score.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
- use strict;
---- ensembl-57.orig/ensembl-compara/scripts/BLAT/fastafetch.pl
-+++ ensembl-57/ensembl-compara/scripts/BLAT/fastafetch.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/BLAT/LoadBLATAlignments.pl
-+++ ensembl-57/ensembl-compara/scripts/BLAT/LoadBLATAlignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::GenomicAlignBlock;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadMapAnchors.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadMapAnchors.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Data::Dumper;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/get_stats.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/get_stats.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaConvertSchema.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaConvertSchema.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/check_genetree_data.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/check_genetree_data.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- =pod
-
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaLoadGenomes.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaLoadGenomes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadHomologySystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadHomologySystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaLoadMembers.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaLoadMembers.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadPairAlignerSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadPairAlignerSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadLowCoverageAlignerSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadLowCoverageAlignerSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/load2xAlignmentFilterSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/load2xAlignmentFilterSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaDumpAllPeptides.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaDumpAllPeptides.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/LaunchBlastRunnable.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/LaunchBlastRunnable.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- $| = 1;
-
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaDumpGenes.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaDumpGenes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/update_genome.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/update_genome.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/dumpDnaFragChunks.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/dumpDnaFragChunks.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Switch;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadEHMMSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadEHMMSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/merge_protein_data.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/merge_protein_data.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadChainNetSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadChainNetSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaLoadHomology.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaLoadHomology.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadMultipleAlignerSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadMultipleAlignerSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGenerateAnchors.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadGenerateAnchors.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Data::Dumper;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster_tablereuse.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/loadGeneTreeSystem.hcluster_tablereuse.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/pipeline/comparaTest.pl
-+++ ensembl-57/ensembl-compara/scripts/pipeline/comparaTest.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use DBI;
---- ensembl-57.orig/ensembl-compara/scripts/gen_malign/test_GenomicAlignAdaptor.pl
-+++ ensembl-57/ensembl-compara/scripts/gen_malign/test_GenomicAlignAdaptor.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::GenomicAlign;
---- ensembl-57.orig/ensembl-compara/scripts/gen_malign/store_mavid_alignment.pl
-+++ ensembl-57/ensembl-compara/scripts/gen_malign/store_mavid_alignment.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- my $description = q{
- ###############################################################################
---- ensembl-57.orig/ensembl-compara/scripts/gen_malign/store_multiz_alignment.pl
-+++ ensembl-57/ensembl-compara/scripts/gen_malign/store_multiz_alignment.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- my $description = q{
- ###############################################################################
---- ensembl-57.orig/ensembl-compara/scripts/gen_malign/test_MethodLinkSpeciesSetAdaptor.pl
-+++ ensembl-57/ensembl-compara/scripts/gen_malign/test_MethodLinkSpeciesSetAdaptor.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
---- ensembl-57.orig/ensembl-compara/scripts/gen_malign/check_mavid_alignments.pl
-+++ ensembl-57/ensembl-compara/scripts/gen_malign/check_mavid_alignments.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- my $description = q{
- ###############################################################################
---- ensembl-57.orig/ensembl-compara/scripts/gen_malign/store_old_pairwise_alignments_into_new_schema.pl
-+++ ensembl-57/ensembl-compara/scripts/gen_malign/store_old_pairwise_alignments_into_new_schema.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- my $description = q{
- ###############################################################################
---- ensembl-57.orig/ensembl-compara/scripts/hcr/CleanLSFHeaders.pl
-+++ ensembl-57/ensembl-compara/scripts/hcr/CleanLSFHeaders.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl-compara/scripts/hcr/subsetAxtFromAndToCompara.pl
-+++ ensembl-57/ensembl-compara/scripts/hcr/subsetAxtFromAndToCompara.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::Registry;
---- ensembl-57.orig/ensembl-compara/scripts/phusion/GetExtra.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/GetExtra.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # This script, originally written by Jim Mullikin, then called PhusionBlastExtra.pl was renamed to GetExtra.pl
- # with no code modification
---- ensembl-57.orig/ensembl-compara/scripts/phusion/fasta2tag.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/fasta2tag.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # This script, originally written by Jim Mullikin, then called tagFA.pl was remaned to fasta2tag.pl
- # with no code modification
---- ensembl-57.orig/ensembl-compara/scripts/phusion/CheckMetaTable.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/CheckMetaTable.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/phusion/LaunchBlast.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/LaunchBlast.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/phusion/RemoveNonSyntenic.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/RemoveNonSyntenic.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # This script, originally written by Jim Mullikin, then called rmRedunGComp.pl was remaned to RemoveNonSyntenic.pl
- # with no code modification
---- ensembl-57.orig/ensembl-compara/scripts/phusion/LoadComparaDb.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/LoadComparaDb.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/phusion/FilterBlast.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/FilterBlast.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # This script, originally written by Jim Mullikin, then called cigar.pl was renamed to FilterBlast.pl
- # and adapted to also filter wutblastx outputs
---- ensembl-57.orig/ensembl-compara/scripts/phusion/DispatchExtra.pl
-+++ ensembl-57/ensembl-compara/scripts/phusion/DispatchExtra.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/scripts/initialize/add_MethodLinkSpeciesSet.pl
-+++ ensembl-57/ensembl-compara/scripts/initialize/add_MethodLinkSpeciesSet.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-compara/docs/create_mlss_table.pl
-+++ ensembl-57/ensembl-compara/docs/create_mlss_table.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- my $description = q{
- ###########################################################################
---- ensembl-57.orig/ensembl-external/scripts/fetchSNP.pl
-+++ ensembl-57/ensembl-external/scripts/fetchSNP.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor;
- use Bio::EnsEMBL::ExternalData::Variation;
---- ensembl-57.orig/ensembl-external/family/src/markov/markovmatrix.pl
-+++ ensembl-57/ensembl-external/family/src/markov/markovmatrix.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- $|=1;
- use POSIX;
- $i=0;
---- ensembl-57.orig/ensembl-external/family/scripts/parse_mcl.pl
-+++ ensembl-57/ensembl-external/family/scripts/parse_mcl.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- # $Id: parse_mcl.pl,v 1.6 2003-06-23 14:35:34 mcvicker Exp $
-
- # Parse MCL output (numbers) back into real clusters (with protein names)
---- ensembl-57.orig/ensembl-external/family/scripts/InsertGenesInFamilies.pl
-+++ ensembl-57/ensembl-external/family/scripts/InsertGenesInFamilies.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-external/family/scripts/LaunchClustalwOnFamilies.pl
-+++ ensembl-57/ensembl-external/family/scripts/LaunchClustalwOnFamilies.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-external/family/scripts/LaunchBlast.pl
-+++ ensembl-57/ensembl-external/family/scripts/LaunchBlast.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-external/family/scripts/LoadSeqInFamily.pl
-+++ ensembl-57/ensembl-external/family/scripts/LoadSeqInFamily.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-external/family/scripts/consensifier.pl
-+++ ensembl-57/ensembl-external/family/scripts/consensifier.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- # $Id: consensifier.pl,v 1.7 2003-05-27 09:12:06 abel Exp $
- #
- # Derives consensus annotations from descriptions in a database, using a
---- ensembl-57.orig/ensembl-external/family/scripts/assemble-consensus.pl
-+++ ensembl-57/ensembl-external/family/scripts/assemble-consensus.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- # Script to assembl the consensus annotations from different files into
- # final ones. It basically takes the SWISS-PROT description consensus if
---- ensembl-57.orig/ensembl-external/family/scripts/GetSeqAndDescription.pl
-+++ ensembl-57/ensembl-external/family/scripts/GetSeqAndDescription.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-external/family/scripts/family-id-map.pl
-+++ ensembl-57/ensembl-external/family/scripts/family-id-map.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- #
- # Usage:
- #
---- ensembl-57.orig/ensembl-external/family/scripts/SplitPeptides.pl
-+++ ensembl-57/ensembl-external/family/scripts/SplitPeptides.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-external/family/scripts/LoadDescriptionInFamily.pl
-+++ ensembl-57/ensembl-external/family/scripts/LoadDescriptionInFamily.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl-external/family/scripts/dumpTranslation.pl
-+++ ensembl-57/ensembl-external/family/scripts/dumpTranslation.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
-
---- ensembl-57.orig/modules/GO/CGI/HTMLTemplate.pm
-+++ ensembl-57/modules/GO/CGI/HTMLTemplate.pm
-@@ -6,7 +6,7 @@
- #
- # You may distribute this module under the same terms as perl itself
-
--#!/usr/local/bin/perl5.6.0 -w
-+#!/usr/bin/perl5.6.0 -w
- package GO::CGI::HTMLTemplate;
- use GO::Utils qw(rearrange);
- use XML::Writer;
---- ensembl-57.orig/modules/GO/CGI/Session.pm
-+++ ensembl-57/modules/GO/CGI/Session.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- #
- =head1 usage
-
---- ensembl-57.orig/modules/GO/IO/Fasta.pm
-+++ ensembl-57/modules/GO/IO/Fasta.pm
-@@ -7,7 +7,7 @@
- #
- # You may distribute this module under the same terms as perl itself
-
--#!/usr/local/bin/perl5.6.0 -w
-+#!/usr/bin/perl5.6.0 -w
- package GO::IO::Fasta;
-
- =head1 NAME
---- ensembl-57.orig/modules/GO/IO/XML.pm
-+++ ensembl-57/modules/GO/IO/XML.pm
-@@ -7,7 +7,7 @@
- #
- # You may distribute this module under the same terms as perl itself
-
--#!/usr/local/bin/perl5.6.0 -w
-+#!/usr/bin/perl5.6.0 -w
- package GO::IO::XML;
-
- =head1 NAME
---- ensembl-57.orig/modules/GO/IO/HTML.pm
-+++ ensembl-57/modules/GO/IO/HTML.pm
-@@ -5,7 +5,7 @@
- #
- # You may distribute this module under the same terms as perl itself
- #
--#!/usr/local/bin/perl5.6.0 -w
-+#!/usr/bin/perl5.6.0 -w
- package GO::IO::HTML;
- use GO::CGI::HTMLTemplate;
- use GO::CGI::NameMunger;
---- ensembl-57.orig/modules/EnsEMBL/Web/ExtIndex.pm
-+++ ensembl-57/modules/EnsEMBL/Web/ExtIndex.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- package EnsEMBL::Web::ExtIndex;
- use EnsEMBL::Web::Root;
---- ensembl-57.orig/modules/EnsEMBL/Web/ExternalDAS.pm
-+++ ensembl-57/modules/EnsEMBL/Web/ExternalDAS.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- package EnsEMBL::Web::ExternalDAS;
- use strict;
---- ensembl-57.orig/modules/EnsEMBL/Web/Tools/DHTMLmerge.pm
-+++ ensembl-57/modules/EnsEMBL/Web/Tools/DHTMLmerge.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- ###############################################################################
- #
- # Name: EnsEMBL::Web::Tools::DHTMLmerge
---- ensembl-57.orig/modules/EnsEMBL/Web/ExtIndex/WEBSRS.pm
-+++ ensembl-57/modules/EnsEMBL/Web/ExtIndex/WEBSRS.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- package EnsEMBL::Web::ExtIndex::WEBSRS;
- require LWP::UserAgent;
---- ensembl-57.orig/modules/EnsEMBL/Web/ExtIndex/bioperl.pm
-+++ ensembl-57/modules/EnsEMBL/Web/ExtIndex/bioperl.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- package EnsEMBL::Web::ExtIndex::bioperl;
- use strict;
---- ensembl-57.orig/modules/EnsEMBL/Web/BlastView/BlastDefs.pm
-+++ ensembl-57/modules/EnsEMBL/Web/BlastView/BlastDefs.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- #======================================================================
- #
- # Name: BlastDefs.pm
---- ensembl-57.orig/ensembl-functgenomics/scripts/update_regulatory_feature_types.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/update_regulatory_feature_types.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
- use strict;
---- ensembl-57.orig/ensembl-functgenomics/scripts/load_pf.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/load_pf.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use warnings;
- use strict;
---- ensembl-57.orig/ensembl-functgenomics/scripts/check_displayable_features.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/check_displayable_features.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
-
- use strict;
---- ensembl-57.orig/ensembl-functgenomics/scripts/import/import_coord_systems.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/import/import_coord_systems.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use warnings;
- use strict;
---- ensembl-57.orig/ensembl-functgenomics/scripts/import/import_design.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/import/import_design.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- ####!/opt/local/bin/perl -w
-
---- ensembl-57.orig/ensembl-functgenomics/scripts/export/get_data.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/export/get_data.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
-
- #Add pod docs here!
---- ensembl-57.orig/ensembl-functgenomics/scripts/export/dump_genes.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/export/dump_genes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl-functgenomics/scripts/export/dump_gff_features.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/export/dump_gff_features.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use warnings;
- use strict;
---- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/reg_feat_gen_feat_overlaps.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/reg_feat_gen_feat_overlaps.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- =head1 DESCRIPTION
-
---- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/reg_feats_4_classification.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/reg_feats_4_classification.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- =head1 DESCRIPTION
-
---- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/gen_feats_4_classification.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/gen_feats_4_classification.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- =head1 DESCRIPTION
-
---- ensembl-57.orig/ensembl-functgenomics/scripts/regulatory_annotation/mock_reg_feat_gen.pl
-+++ ensembl-57/ensembl-functgenomics/scripts/regulatory_annotation/mock_reg_feat_gen.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 DESCRIPTION
-
---- ensembl-57.orig/conf/SiteDefs.pm
-+++ ensembl-57/conf/SiteDefs.pm
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- ###############################################################################
- #
- # Name: SiteDefs.pm
---- ensembl-57.orig/ensembl/misc-scripts/CreateFile4CopyDBoverServer.pl
-+++ ensembl-57/ensembl/misc-scripts/CreateFile4CopyDBoverServer.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- ##########################################
- #
- # Simple but handy script that generate the input file
---- ensembl-57.orig/ensembl/misc-scripts/translation_attribs.pl
-+++ ensembl-57/ensembl/misc-scripts/translation_attribs.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/translation_attribs_wrapper.pl
-+++ ensembl-57/ensembl/misc-scripts/translation_attribs_wrapper.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/update_mapping_set.pl
-+++ ensembl-57/ensembl/misc-scripts/update_mapping_set.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/constitutive_exon.pl
-+++ ensembl-57/ensembl/misc-scripts/constitutive_exon.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl/misc-scripts/meta_levels.pl
-+++ ensembl-57/ensembl/misc-scripts/meta_levels.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # Populate meta table with (e.g.) genebuild.level = toplevel if all genes are
- # top level. Using v41 API code this can speed fetching & dumping greatly.
---- ensembl-57.orig/ensembl/misc-scripts/CopyDBoverServer.pl
-+++ ensembl-57/ensembl/misc-scripts/CopyDBoverServer.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl/misc-scripts/schema_patch.pl
-+++ ensembl-57/ensembl/misc-scripts/schema_patch.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl/misc-scripts/add_species_aliases.pl
-+++ ensembl-57/ensembl/misc-scripts/add_species_aliases.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl/misc-scripts/overlapping_regions.pl
-+++ ensembl-57/ensembl/misc-scripts/overlapping_regions.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/search_dbs.pl
-+++ ensembl-57/ensembl/misc-scripts/search_dbs.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # this script will lokk through all listed databases for
- # database names which match given regexp.
---- ensembl-57.orig/ensembl/misc-scripts/db-space.pl
-+++ ensembl-57/ensembl/misc-scripts/db-space.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl/misc-scripts/attribute_types/upload_attributes.pl
-+++ ensembl-57/ensembl/misc-scripts/attribute_types/upload_attributes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- #
- # Stolen from external db directory this script performs
- # the similar function of uploading all valid attribute types
---- ensembl-57.orig/ensembl/misc-scripts/utilities/dna_compress.pl
-+++ ensembl-57/ensembl/misc-scripts/utilities/dna_compress.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -- # -*-Perl-*-
-+#!/usr/bin/perl -- # -*-Perl-*-
- #
- # Copyright (c) 2003 Tim Hubbard (th at sanger.ac.uk)
- # Sanger Centre, Wellcome Trust Genome Campus, Cambs, UK
---- ensembl-57.orig/ensembl/misc-scripts/utilities/show_method_status.pl
-+++ ensembl-57/ensembl/misc-scripts/utilities/show_method_status.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/canonical_transcripts/set_canonical_transcripts.pl
-+++ ensembl-57/ensembl/misc-scripts/canonical_transcripts/set_canonical_transcripts.pl
-@@ -23,7 +23,7 @@ EXTRA
-
- =cut
-
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Carp;
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/dump_cache.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/dump_cache.pl
-@@ -1,5 +1,5 @@
- #!/software/bin/perl
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/synteny_rescore.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/synteny_rescore.pl
-@@ -1,5 +1,5 @@
- #!/software/bin/perl
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/run.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/run.pl
-@@ -1,5 +1,5 @@
- #!/software/bin/perl
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/id_mapping.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/id_mapping.pl
-@@ -1,5 +1,5 @@
- #!/software/bin/perl
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/fake_stable_id_mapping.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/fake_stable_id_mapping.pl
-@@ -1,5 +1,5 @@
- #!/software/bin/perl
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/dump_by_seq_region.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/dump_by_seq_region.pl
-@@ -1,5 +1,5 @@
- #!/software/bin/perl
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/batch_id_history.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/batch_id_history.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/dump_scores.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/dump_scores.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/compare_scores.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/compare_scores.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/id_mapping/utils/compare_results.pl
-+++ ensembl-57/ensembl/misc-scripts/id_mapping/utils/compare_results.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/analysis_description/chech_web_data_column.pl
-+++ ensembl-57/ensembl/misc-scripts/analysis_description/chech_web_data_column.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =pod
-
---- ensembl-57.orig/ensembl/misc-scripts/analysis_description/apply_rules.pl
-+++ ensembl-57/ensembl/misc-scripts/analysis_description/apply_rules.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- ###!/usr/local/ensembl/bin/perl
-
- # POD documentation - main docs before the code
---- ensembl-57.orig/ensembl/misc-scripts/analysis_description/load_analysis_descriptions.pl
-+++ ensembl-57/ensembl/misc-scripts/analysis_description/load_analysis_descriptions.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # POD documentation - main docs before the code
-
---- ensembl-57.orig/ensembl/misc-scripts/ebi_search_dump/ebi_search_dump.pl
-+++ ensembl-57/ensembl/misc-scripts/ebi_search_dump/ebi_search_dump.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- # Dump variation information to an XML file for indexing by the EBI's search engine.
- #
---- ensembl-57.orig/ensembl/misc-scripts/repeats/vega_repeat_libraries.pl
-+++ ensembl-57/ensembl/misc-scripts/repeats/vega_repeat_libraries.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/external_db/update_external_dbs.pl
-+++ ensembl-57/ensembl/misc-scripts/external_db/update_external_dbs.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #
- # updates the external db tables on all of the core databases on a given host
---- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/xref_tracker.pl
-+++ ensembl-57/ensembl/misc-scripts/xref_mapping/xref_tracker.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
-
- use strict;
---- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/xref_mapper.pl
-+++ ensembl-57/ensembl/misc-scripts/xref_mapping/xref_mapper.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
-
- use strict;
---- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/xref_config2sql.pl
-+++ ensembl-57/ensembl/misc-scripts/xref_mapping/xref_config2sql.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # $Id: xref_config2sql.pl,v 1.14 2009-11-19 12:56:07 ianl Exp $
-
---- ensembl-57.orig/ensembl/misc-scripts/xref_mapping/test_xref_mapper.pl
-+++ ensembl-57/ensembl/misc-scripts/xref_mapping/test_xref_mapper.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/density_feature/gene_density_calc.pl
-+++ ensembl-57/ensembl/misc-scripts/density_feature/gene_density_calc.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #
- # script to calculate the gene density features on a database
---- ensembl-57.orig/ensembl/misc-scripts/density_feature/percent_gc_calc.pl
-+++ ensembl-57/ensembl/misc-scripts/density_feature/percent_gc_calc.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #
- # Calculate the GC content for top level seq_regions
---- ensembl-57.orig/ensembl/misc-scripts/density_feature/variation_density.pl
-+++ ensembl-57/ensembl/misc-scripts/density_feature/variation_density.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #
- # calculates the variation density from given core database
---- ensembl-57.orig/ensembl/misc-scripts/density_feature/density_feature_fetch.pl
-+++ ensembl-57/ensembl/misc-scripts/density_feature/density_feature_fetch.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #
- # Ignore file anme this should calculate the gene count for a chromosome (X)
---- ensembl-57.orig/ensembl/misc-scripts/density_feature/glovar_snp_density.pl
-+++ ensembl-57/ensembl/misc-scripts/density_feature/glovar_snp_density.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/density_feature/repeat_coverage_calc.pl
-+++ ensembl-57/ensembl/misc-scripts/density_feature/repeat_coverage_calc.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- #
- # Calculate the repeat coverage for given database.
- # condition: 1k blocks to show contigview displays
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/dump_genebank.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/dump_genebank.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/dump_genbank_45.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/dump_genbank_45.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/location_check_for_dump.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/location_check_for_dump.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- ## check of old and new protein positions, to see where old & new versions of the same transcript are in different (non-overlapping) positions - identifies 50 on same chr of which just 16 are same scaffold (identified manually - should incorporate this in script!) Currently set so STDOUT prints just those that have jumped location within a chromosome (where chromosome includes UNKN)
-
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/protein_annotation_from_embl.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/protein_annotation_from_embl.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # script to pull selected protein annotation from an EMBL scaffold entry
- # point to file with all 69724 anopheles scaffolds/contigs
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/load_karyotype.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/load_karyotype.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- =head1 NAME
-
-
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/remove_proteins_from_db.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/remove_proteins_from_db.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # script to remove proteins from core database
- # leaves transcript and tags gene as bacterial contaminant
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/check_stops.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/check_stops.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/split_fasta_in_subslices_anopheles.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/split_fasta_in_subslices_anopheles.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # Written by Jan-Hinnerk Vogel, modifed by mh4
- #
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/dump_genebank_38.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/dump_genebank_38.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Getopt::Long;
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/get_transposon_repeats.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/get_transposon_repeats.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- =head1 NAME
-
- delete_genes.pl
---- ensembl-57.orig/ensembl/misc-scripts/anopheles_scripts/produce_snap_training_set.pl
-+++ ensembl-57/ensembl/misc-scripts/anopheles_scripts/produce_snap_training_set.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/load_OBO_file.pl
-+++ ensembl-57/ensembl/misc-scripts/ontology/scripts/load_OBO_file.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # A simple OBO file reader/loader
- # for parsing/loading OBO files from (at least) GO and SO
---- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/demo1.pl
-+++ ensembl-57/ensembl/misc-scripts/ontology/scripts/demo1.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #-----------------------------------------------------------------------
- # Demo program for the Ensembl ontology database and API.
---- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/compute_closure.pl
-+++ ensembl-57/ensembl/misc-scripts/ontology/scripts/compute_closure.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # Modified from "Relational Modeling of
- # Biological Data: Trees and Graphs", page 2:
---- ensembl-57.orig/ensembl/misc-scripts/ontology/scripts/demo2.pl
-+++ ensembl-57/ensembl/misc-scripts/ontology/scripts/demo2.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #-----------------------------------------------------------------------
- # Demo program for the Ensembl ontology database and API.
---- ensembl-57.orig/ensembl/misc-scripts/alternative_splicing/Fetch_gff.pl
-+++ ensembl-57/ensembl/misc-scripts/alternative_splicing/Fetch_gff.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- =head1 LICENSE
-
---- ensembl-57.orig/ensembl/misc-scripts/meta_coord/update_meta_coord.pl
-+++ ensembl-57/ensembl/misc-scripts/meta_coord/update_meta_coord.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use Bio::EnsEMBL::DBSQL::DBConnection;
---- ensembl-57.orig/ensembl/misc-scripts/assembly/find_overlaps.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/find_overlaps.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/EXAMPLE.use_mapping.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/EXAMPLE.use_mapping.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/align_nonident_regions.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/align_nonident_regions.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/compare_assemblies.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/compare_assemblies.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/check_mapping.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/check_mapping.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/fix_overlaps.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/fix_overlaps.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/load_alternative_assembly.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/load_alternative_assembly.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/mapping_stats.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/mapping_stats.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/align_by_clone_identity.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/align_by_clone_identity.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/assembly/align_nonident_regions_wrapper.pl
-+++ ensembl-57/ensembl/misc-scripts/assembly/align_nonident_regions_wrapper.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/db/cleanup_tmp_tables.pl
-+++ ensembl-57/ensembl/misc-scripts/db/cleanup_tmp_tables.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- =head1 NAME
-
---- ensembl-57.orig/ensembl/misc-scripts/golden_path/nt_crossmatch.pl
-+++ ensembl-57/ensembl/misc-scripts/golden_path/nt_crossmatch.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- #This script reads a file which has nt contig and clone coordinates
- #then reads a fasta file of all nt contigs
---- ensembl-57.orig/ensembl/misc-scripts/golden_path/check_sum.pl
-+++ ensembl-57/ensembl/misc-scripts/golden_path/check_sum.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- while(<>) {
- chomp;
- ($f,$c,$rid,$cstart,$cend,$fstart,$fend,$rstart,$rend,$ori,$type) = split;
---- ensembl-57.orig/ensembl/misc-scripts/golden_path/makeunique.pl
-+++ ensembl-57/ensembl/misc-scripts/golden_path/makeunique.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- open(ERROR,">nonunique.txt");
-
---- ensembl-57.orig/ensembl/misc-scripts/misc_feature/update_misc_set_descripitons.pl
-+++ ensembl-57/ensembl/misc-scripts/misc_feature/update_misc_set_descripitons.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- # POD documentation - main docs before the code
-
---- ensembl-57.orig/ensembl-variation/scripts/import/parse_association.pl
-+++ ensembl-57/ensembl-variation/scripts/import/parse_association.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- #use DBH;
---- ensembl-57.orig/ensembl-variation/scripts/import/dbSNP.pl
-+++ ensembl-57/ensembl-variation/scripts/import/dbSNP.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- # this is the script to fill the new variation
- # schema with data from dbSNP
- # we use the local mssql copy of dbSNP at the sanger center
---- ensembl-57.orig/ensembl-variation/scripts/import/make_index_files.pl
-+++ ensembl-57/ensembl-variation/scripts/import/make_index_files.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/read_coverage.pl
-+++ ensembl-57/ensembl-variation/scripts/import/read_coverage.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/parse_hapmap_genotye.pl
-+++ ensembl-57/ensembl-variation/scripts/import/parse_hapmap_genotye.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- # this script read hapmap genotyping data into individual,
- #individual_genotype, population, population_genotype tables
-
---- ensembl-57.orig/ensembl-variation/scripts/import/dump_strain_seq.pl
-+++ ensembl-57/ensembl-variation/scripts/import/dump_strain_seq.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/tag_snps.pl
-+++ ensembl-57/ensembl-variation/scripts/import/tag_snps.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/import_wrapper.pl
-+++ ensembl-57/ensembl-variation/scripts/import/import_wrapper.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/select_tag_snps.pl
-+++ ensembl-57/ensembl-variation/scripts/import/select_tag_snps.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/ensembl-variation/scripts/import/create_ld_table.pl
-+++ ensembl-57/ensembl-variation/scripts/import/create_ld_table.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/ensembl-variation/scripts/import/upgrade_resequencing_files.pl
-+++ ensembl-57/ensembl-variation/scripts/import/upgrade_resequencing_files.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/calculate_ld_table.pl
-+++ ensembl-57/ensembl-variation/scripts/import/calculate_ld_table.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/ensembl-variation/scripts/import/compress_genotypes.pl
-+++ ensembl-57/ensembl-variation/scripts/import/compress_genotypes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/ensembl-variation/scripts/import/calc_genotypes.pl
-+++ ensembl-57/ensembl-variation/scripts/import/calc_genotypes.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- =head1 Docs
-
---- ensembl-57.orig/ensembl-variation/scripts/import/dump_strain_seq_1kg.pl
-+++ ensembl-57/ensembl-variation/scripts/import/dump_strain_seq_1kg.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/parallel_read_coverage.pl
-+++ ensembl-57/ensembl-variation/scripts/import/parallel_read_coverage.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/compress_genotypes_by_seq_region.pl
-+++ ensembl-57/ensembl-variation/scripts/import/compress_genotypes_by_seq_region.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/ensembl-variation/scripts/import/dump_strain_wrapper.pl
-+++ ensembl-57/ensembl-variation/scripts/import/dump_strain_wrapper.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/dbSNP_submission.pl
-+++ ensembl-57/ensembl-variation/scripts/import/dbSNP_submission.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/ensembl-variation/scripts/import/load_mapping2vf.pl
-+++ ensembl-57/ensembl-variation/scripts/import/load_mapping2vf.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
- # this script read mapping data ALL_DIFF into variation_feature table
-
- use strict;
---- ensembl-57.orig/ensembl-variation/scripts/import/import_cnv.pl
-+++ ensembl-57/ensembl-variation/scripts/import/import_cnv.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- #to run it type perl import_cnv.pl data_file.txt
- use strict;
---- ensembl-57.orig/ensembl-variation/scripts/import/import_Sanger_database.pl
-+++ ensembl-57/ensembl-variation/scripts/import/import_Sanger_database.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/Solexa/import_Solexa.pl
-+++ ensembl-57/ensembl-variation/scripts/import/Solexa/import_Solexa.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/Sanger/import_Sanger_database.pl
-+++ ensembl-57/ensembl-variation/scripts/import/Sanger/import_Sanger_database.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/ensembl-variation/scripts/import/LRG/lrg_import_export.pl
-+++ ensembl-57/ensembl-variation/scripts/import/LRG/lrg_import_export.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/ensembl/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/utils/show_features.pl
-+++ ensembl-57/utils/show_features.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use FindBin qw($Bin);
- use File::Basename qw(dirname);
---- ensembl-57.orig/utils/parse_blast.pl
-+++ ensembl-57/utils/parse_blast.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
-
---- ensembl-57.orig/utils/initialise_das.pl
-+++ ensembl-57/utils/initialise_das.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- # This script generates static content (e.g. sources document)
- # for DAS. Unfortunately lots of strange things have to happen to map between
---- ensembl-57.orig/utils/memd.pl
-+++ ensembl-57/utils/memd.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use FindBin qw($Bin);
---- ensembl-57.orig/utils/test_blast_api.pl
-+++ ensembl-57/utils/test_blast_api.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
- use warnings;
- use Carp;
---- ensembl-57.orig/utils/make-image-index.pl
-+++ ensembl-57/utils/make-image-index.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use Image::Size;
---- ensembl-57.orig/utils/runblast.pl
-+++ ensembl-57/utils/runblast.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/utils/pack_species.pl
-+++ ensembl-57/utils/pack_species.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- #package EnsEMBL::Web::config_packer;
- use FindBin qw($Bin);
---- ensembl-57.orig/utils/css-js-cleaner.pl
-+++ ensembl-57/utils/css-js-cleaner.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
-
---- ensembl-57.orig/utils/blast_database.pl
-+++ ensembl-57/utils/blast_database.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/utils/blast_cleaner.pl
-+++ ensembl-57/utils/blast_cleaner.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- use strict;
- use warnings;
---- ensembl-57.orig/utils/remove_sleeping_blast.pl
-+++ ensembl-57/utils/remove_sleeping_blast.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
-
- #remove all sleeping blast jobs older than 1000s
-
---- ensembl-57.orig/utils/static_content/eg_homepages.pl
-+++ ensembl-57/utils/static_content/eg_homepages.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- ## Script to generate species' home pages
-
---- ensembl-57.orig/utils/static_content/make_encode_table.pl
-+++ ensembl-57/utils/static_content/make_encode_table.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use FindBin qw($Bin);
---- ensembl-57.orig/utils/static_content/update_webdb.pl
-+++ ensembl-57/utils/static_content/update_webdb.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/utils/static_content/create_helplinktable.pl
-+++ ensembl-57/utils/static_content/create_helplinktable.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use strict;
- use warnings;
---- ensembl-57.orig/utils/static_content/sample_links.pl
-+++ ensembl-57/utils/static_content/sample_links.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- #############################################################################
- #
---- ensembl-57.orig/utils/static_content/psychic_search.pl
-+++ ensembl-57/utils/static_content/psychic_search.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- ## Script to output "psychic search" inserts for all species' home pages
-
---- ensembl-57.orig/utils/static_content/species_stats.pl
-+++ ensembl-57/utils/static_content/species_stats.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- ##############################################################################
- #
---- ensembl-57.orig/utils/server_maintenance/last_script.pl
-+++ ensembl-57/utils/server_maintenance/last_script.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- ### A short script which parses an error log and reports the PID
- ### of the child along with the last SCRIPT/ENDSCR line in the
-@@ -24,7 +24,7 @@ foreach my $K (sort keys %X) {
- }
-
- [w3adm at web-3-02 utils]$ cat last_script.pl
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
- use strict;
-
- my %X = ();
---- ensembl-57.orig/utils/server_maintenance/count_warns.pl
-+++ ensembl-57/utils/server_maintenance/count_warns.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- ### A small script which looks through an error log file
- ### and for each warn line in the logs reports the
---- ensembl-57.orig/utils/edoc/update_docs.pl
-+++ ensembl-57/utils/edoc/update_docs.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl
-+#!/usr/bin/perl
-
- use FindBin qw($Bin);
- use File::Basename qw(dirname);
---- ensembl-57.orig/utils/spider/spider.pl
-+++ ensembl-57/utils/spider/spider.pl
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/perl -w
- use strict;
- #no warnings;
-
Modified: trunk/packages/ensembl/ensembl/57/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-20 22:57:12 UTC (rev 5177)
+++ trunk/packages/ensembl/ensembl/57/debian/patches/series 2010-08-20 23:12:28 UTC (rev 5178)
@@ -1,4 +1,3 @@
-debian-changes-57-1
calc_genotypes_config.patch
apache_mods.patch
species_list.patch
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